changes in reorder(, "cladewise")

[ape.git] / R / reorder.phylo.R

diff --git a/R/reorder.phylo.R b/R/reorder.phylo.R
index 226adb946c334f048382f0f04083429de3d4078d..c7e11d3bb5c4816d4dadccaf9fc69935060fd4ed 100644 (file)
--- a/R/reorder.phylo.R
+++ b/R/reorder.phylo.R
@@ -1,4 +1,4 @@
-## reorder.phylo.R (2012-08-01)
+## reorder.phylo.R (2012-08-17)
 
 ##   Internal Reordering of Trees
 
@@ -21,7 +21,7 @@ reorder.phylo <- function(x, order = "cladewise", ...)
             .C("neworder_cladewise", as.integer(nb.tip),
                as.integer(x$edge[, 1]), as.integer(x$edge[, 2]),
                as.integer(nb.edge), integer(nb.edge),
-               PACKAGE = "ape")[[5]]
+               DUP = FALSE, NAOK = TRUE, PACKAGE = "ape")[[5]]
     } else {
         ##node.degree <- tabulate(x$edge[, 1])
         neworder <-
@@ -29,7 +29,7 @@ reorder.phylo <- function(x, order = "cladewise", ...)
                as.integer(nb.node), as.integer(x$edge[, 1]),
                as.integer(x$edge[, 2]), as.integer(nb.edge),
                integer(nb.edge), PACKAGE = "ape")[[6]]
-  }
+    }
     x$edge <- x$edge[neworder, ]
     if (!is.null(x$edge.length))
       x$edge.length <- x$edge.length[neworder]